From 67293168e78ebcb3ded414d5a81c7a575abf917f Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 May 2009 20:17:57 +0000
Subject: [PATCH] Support periods in sequence names.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@715 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/utils/fasta/FastaSequenceIndex.java    | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
index 89b25ccc1..79c982999 100755
--- a/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/FastaSequenceIndex.java
@@ -48,7 +48,7 @@ public class FastaSequenceIndex implements Iterable {
 
         while( scanner.hasNext() ) {
             // Tokenize and validate the index line.
-            String result = scanner.findInLine("(\\w+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
+            String result = scanner.findInLine("([\\w\\.]+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)\\s+(\\d+)");
             if( result == null )
                 throw new PicardException("Found invalid line in index file:" + scanner.nextLine());
             MatchResult tokens = scanner.match();